Class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest

all > org.broadinstitute.hellbender.cmdline.GATKPlugin > GATKAnnotationPluginDescriptorUnitTest
48

tests
0

failures
0

ignored
1.926s

duration
100%

successful

Tests

Test Duration Result
testAnnotationArguments 0.029s passed
testAnnotationGroupAdditive 0.006s passed
testConfigFileControlsAnnotationPackages 1.737s passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1) 0.006s passed
testGetAllowedValuesForDescriptorHelpGroups 0.003s passed
testGetAllowedValuesForDescriptorHelp[0]([]) 0.005s passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@25dad235]) 0.004s passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@771cbd13, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@229749f0]) 0.004s passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@1013871e, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@5a9051fd]) 0.003s passed
testGetClassForPluginHelpFromReflection 0.003s passed
testGetDefaultInstances 0.004s passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@65a80fdb, false, false) 0.003s passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@5b55c3d6, true, true) 0.003s passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@2059f785, true, false) 0.003s passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@771d4db, true, true) 0.003s passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@1397b141, true, true) 0.003s passed
testHierarchicalAnnotationDiscovery 0.001s passed
testIncludeAllExcludeIndividual 0.012s passed
testIncludeDefaultExcludeIndividual 0.003s passed
testIncludeDefaultGroupExcludeIndividual 0.003s passed
testIncludeUserGroupExcludeIndividual 0.003s passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality]) 0.003s passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation]) 0.002s passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object]) 0.003s passed
testInvalidToolDefaultAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality]) 0s passed
testInvalidToolDefaultAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation]) 0s passed
testInvalidToolDefaultAnnotationGroups[2]([class java.lang.Object]) 0s passed
testInvalidUserSpecifiedAnnotations[0]([-A, StandardAnnotation]) 0.003s passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality]) 0.003s passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality]) 0.003s passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality]) 0.003s passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo]) 0.002s passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator]) 0.002s passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@622ba721, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@6b2f7527], [Ljava.lang.String;@7509226c, true, 5, 0) 0.003s passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@591a4d25, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4bfe83d, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5906ebfb], [Ljava.lang.String;@10fc1a22, true, 5, -0.3333) 0.004s passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@37753b69, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@602c167e, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@74c04377], [Ljava.lang.String;@10d49900, false, 0, 0) 0.003s passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@4d5ea776, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@5d68be4f, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@34eb5d01], [Ljava.lang.String;@77b22b05, true, 5, -0.2941) 0.004s passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@1d008e61, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@191b44ca, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5de243bb], [Ljava.lang.String;@2c4cf7eb, false, 0, -0.3333) 0.003s passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@5db04bd2, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@6f921e32, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@31c5304f], [Ljava.lang.String;@43df1377, false, 0, -0.3333) 0.007s passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@1de6dc80, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@418d1c03, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@395197cb], [Ljava.lang.String;@7305cfb1, true, 5, -0.2941) 0.004s passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@4cb82b09], [Ljava.lang.String;@49665f92, false, 0, -0.2941) 0.006s passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6c56fff], [Ljava.lang.String;@3dee3a6c, false, 0, 0) 0.005s passed
testNoAnnotations 0.003s passed
testOverridingInstancesWithGetInstance 0.001s passed
testPossibleDeNovoAnnotationArguments 0.003s passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine 0.006s passed
testUseAllAnnotations 0.004s passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns 0.005s passed

Standard error

20:13:21.886 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.8.11/13f95ee601084b8bf047b2a37f6ea36cd588b96b/gkl-0.8.11.jar!/com/intel/gkl/native/libgkl_compression.so
SLF4J(W): Class path contains multiple SLF4J providers.
SLF4J(W): Found provider [org.apache.logging.slf4j.SLF4JServiceProvider@67dba613]
SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@57540fd0]
SLF4J(W): See https://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J(I): Actual provider is of type [org.apache.logging.slf4j.SLF4JServiceProvider@67dba613]
20:13:22.003 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:13:22.005 INFO  TestAnnotationsTool - org.broadinstitute.hellbender.cmdline.GATKPlugin vUnavailable
20:13:22.005 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:22.005 INFO  TestAnnotationsTool - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:22.006 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:22.006 INFO  TestAnnotationsTool - Start Date/Time: February 10, 2025 at 8:13:21 PM UTC
20:13:22.006 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:13:22.006 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:13:22.009 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:22.009 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:22.010 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:22.010 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:22.010 INFO  TestAnnotationsTool - Deflater: IntelDeflater
20:13:22.010 INFO  TestAnnotationsTool - Inflater: IntelInflater
20:13:22.011 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
20:13:22.011 INFO  TestAnnotationsTool - Requester pays: disabled
20:13:22.011 INFO  TestAnnotationsTool - Initializing engine
20:13:22.056 INFO  TestAnnotationsTool - Done initializing engine
20:13:22.057 INFO  ProgressMeter - Starting traversal
20:13:22.057 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
20:13:22.060 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
20:13:22.060 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:22.060 INFO  TestAnnotationsTool - Shutting down engine
[February 10, 2025 at 8:13:22 PM UTC] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=146800640
20:13:22.155 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:13:22.164 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:13:22.168 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:13:22.215 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
20:13:22.232 INFO  PedReader - Phenotype is other? false
20:13:22.233 INFO  PedReader - Phenotype is other? false
20:13:22.237 INFO  PedReader - Phenotype is other? false
20:13:22.238 INFO  PedReader - Phenotype is other? false
20:13:22.238 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
20:13:22.250 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
20:13:22.251 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default